9RHM | pdb_00009rhm

Phospho-MCM double hexamer bound to Sld3-Sld7-Cdc45 on ARS1 DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9RHM

This is version 1.2 of the entry. See complete history

Literature

Structure of the pre-initiation complex explains CMGE biogenesis.

Puhringer, T.Canal, B.Palm, G.Butryn, A.Couves, E.C.Willhoft, O.Lewis, J.S.Diffley, J.F.X.Costa, A.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10657-7
  • Primary Citation Related Structures: 
    28VY, 9RHI, 9RHJ, 9RHL, 9RHM

  • PubMed Abstract: 

    When cells enter S phase, bidirectional DNA replication is initiated through the kinase-regulated recruitment of three activators (Cdc45, GINS and Pol ε) to a duplex-DNA-loaded double hexamer of minichromosome maintenance (MCM) ATPases. Together, these proteins form two CMGE helicases that establish divergent replication forks as they become separated 1 . Here, to gain an understanding of CMGE biogenesis, we reconstituted the pre-initiation complex with purified yeast proteins. The cryo-electron-microscopy structure shows a set of firing factors caught in the act of assembling two symmetrical CMGEs. We show how stepwise complex formation reshapes MCM in preparation for DNA opening, and we explain how ATP promotes firing-factor ejection and CMGE maturation. We find that although Sld2 facilitates the recruitment of GINS to MCM, as expected, it also aids the efficient separation of the CMGE dimer, and is essential for the ejection of the lagging strand from MCM. These findings have direct implications for our understanding of the metazoan Sld2 orthologue, RECQL4, and point to a replication-fork establishment mechanism that is conserved across eukaryotes.


  • Organizational Affiliation
    • Macromolecular Machines Laboratory, Francis Crick Institute, London, UK.

Macromolecule Content 

  • Total Structure Weight: 1,552.83 kDa 
  • Atom Count: 68,681 
  • Modeled Residue Count: 8,507 
  • Deposited Residue Count: 13,573 
  • Unique protein chains: 9
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial morphogenesis protein SLD7A,
C [auth R]
257Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD7YOR060CYOR29-11
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication regulator SLD3B [auth H],
F [auth I]
704Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD3YGL113WG2980
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 45G [auth E]657Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2H [auth 2],
N [auth a]
868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3I [auth 3],
O [auth b]
1,006Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4J [auth 4],
P [auth c]
933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5K [auth 5],
Q [auth d]
775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6L [auth 6],
R [auth e]
1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7M [auth 7],
S [auth f]
845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (53-MER)D [auth X]53Saccharomyces cerevisiae
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (53-MER)E [auth Y]53Saccharomyces cerevisiae
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
EA [auth b],
HA [auth d],
U [auth 3],
X [auth 5]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth 6]
BA [auth 7]
CA [auth a]
GA [auth c]
IA [auth d]
AA [auth 6],
BA [auth 7],
CA [auth a],
GA [auth c],
IA [auth d],
JA [auth e],
KA [auth f],
T [auth 2],
W [auth 4],
Z [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth a],
FA [auth b],
V [auth 3],
Y [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001065
The Francis Crick InstituteUnited KingdomFC001066
European Research Council (ERC)European Union820102
Boehringer Ingelheim Fonds (BIF)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-13
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Data collection, Database references
  • Version 1.2: 2026-07-01
    Changes: Data collection, Database references